The flu is simple, right? You get it, you feel terrible and then you get better.
As it turns out, there is a bit more going on at the cellular level. As soon as the virus enters our cells, it hijacks our cell machinery to make copies of itself, followed budding from the host to go infect more cells. Sounds easy right? But it is not! Our cells fight infection by activating various host responses.
During infection, the flu also hijacks various cellular pathways to evade immune surveillance. The flu, for example, antagonizes the pattern-recognition receptor (PPR) pathway. When PPR detects pathogens in our cells, it secretes interferon (IFN), which induces the expression of interferon-stimulated genes (ISGs) and pro-inflammatory cytokines. The flu also modulates the unfolded protein response (UPR). The UPR pathway is activated when cells are subjected to constant insults, such as viral infections, to promote cell death. So, how do viruses trick cells to escape these pathways? Viruses encode viral proteins that can inhibit these pathways. When it comes to flu, the viral protein NS1 blocks the PPR, inhibits IFN secretion and ISG expression, and blocks the UPR. In such a case, is NS1 amount critical to evading cellular pathways? In a recent publication, Dr. Daniel Blanco-Melo, an assistant professor at Fred Hutch, demonstrated that the amount of NS1 that is expressed during flu infection plays a significant role in evading host defenses.
“Influenza A virus (IAV) is an important human respiratory pathogen that causes millions of cases of severe illness each year, and occasionally leads to pandemics,” said Dr. Yang, a postdoctoral fellow in Dr. Blanco-Melo's lab and leader of the study. “IAV deploys multiple strategies to attenuate the host response, most of which are linked to the viral protein NS1,” he added. Their study demonstrates that “NS1 operates as a multifaceted immune modulator, selectively prioritizing specific host pathways crucial for its own replication,” he continued.
To examine the host transcriptome in response to the expression of NS1, the team infected cells with viruses expressing high, intermediate, or no NS1 followed by bulk RNA sequencing. Differential gene expression analysis revealed that the amount of NS1, in part, shapes the host response. An intermediate level of NS1 expression inhibited the production of pro-inflammatory cytokines while failing to inhibit the expression of ISGs. Conversely, high expression of NS1 inhibited the expression of ISGs and UPR target genes. Furthermore, the team examined single cell transcriptomics during flu infection. A cell population was infected with wild type influenza followed by an analysis of NS1 expression in each cell. Individually infected cells were grouped according to their level of NS1 expression. Once again, the team found that NS1 has a significant impact on the host's response. Although intermediate expression of NS1 was sufficient to evade immune detection by inhibiting the expression of pro-inflammatory cytokine genes, high expression of NS1 was necessary to inhibit the expression of ISGs. Additionally, high NS1 expression is required for the inhibition of UPR genes, which are usually activated by the later stages of viral replication. These results suggest that the virus fine tunes the antagonistic potency of NS1 against different host responses to accommodate its replication needs.
“This work not only refines our understanding of NS1's role in immune evasion but also introduces a novel perspective on the hierarchy of host immune pathways targeted by IAV,” said Dr. Young. “The findings have broader implications for antiviral strategies, offering insights into potential vulnerabilities in the virus's immune evasion tactics.”
Going forward the team is interested in identifying the “specific host factors that mediate NS1's differential effects on pathogen sensing, interferon response, and ER stress response” as well as understanding how the “temporal dynamics of NS1 expression correlate with the progression of IAV infection,” and how “these dynamics influence host immune responses over time.” The team would also like to better understand if “different strains of IAV exhibit variability in the host-specificity, frequency, and abundance of NS1 in relation to the magnitude of host response suppression.” They ultimately hope that this research will “help unveil the intricate dynamics of virus-mediated immune antagonism, providing insights for targeted antiviral therapies.”
This work was funded by the University of Washington Department of Global Health T32 postdoctoral training grant, the Deutsche Forschungsgemeinschaft grant, and the Immunology and Vaccine Development Program of the Vaccine and Infectious Disease Division at Fred Hutchinson Cancer Center.
Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium member Dr. Daniel blanco-Melo contributed to this study.
Yang Q, Elz AE, Panis M, Liu T, Nilsson-Payant BE, Blanco-Melo D. 2023. Modulation of Influenza A virus NS1 expression reveals prioritization of host response antagonism at single-cell resolution. Front Microbiol. 14:1267078. doi: 10.3389/fmicb.2023.1267078.